RATIONALE: In-situ SIMS analysis requires the use of standards to unravel the instrumental mass fractionation (IMF) induced by the analytical procedures. Part of this IMF might be caused by the nature of the sample and the differences in composition and structure between the sample and the standards. This "matrix effect" has been tentatively corrected for by using standards with chemical compositions equivalent to the samples, or by the empirical use of chemical parameters. However, these corrections can only be applied to a narrow compositional range and fail to take proper account of the matrix effect when a wider chemical field is tested...

RATIONALE: Koumine is one of the major components of total alkaloids from Gelsemium. And koumine possesses a variety of interesting pharmacological effects, including anti-tumor, anti-inflammatory, and anxiolytic activities. It might be a promising lead drug because of its pharmacological activities and mild toxicity. However, little information is available on the metabolism of koumine. METHODS: A rapid and accurate high-performance liquid chromatography/quadrupole-time -of-flight (HPLC/QqTOF) mass spectrometry method was applied to characterize koumine metabolites...

RATIONALE: Long-chain fatty acyl-Coenzyme As are important bioactive molecules, playing key roles in fatty acids biosynthesis, membrane trafficking and signal transduction. Development of sensitive analytical methods for profiling theses lipid species in various tissues is critical to understand their biological activity. A high pressure liquid chromatography tandem mass spectrometry method has been developed for the quantitative analysis and screening of long-chain fatty acyl-CoAs in liver, brain, muscle and adipose tissue...

RATIONALE: Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) provides detailed and in-depth information about the molecular characteristics of synthetic polymers. To obtain the most accurate results the sample preparation parameters should be chosen to suit the sample and the aim of the experiment. Because the underlying principles of MALDI are still not fully known, a priori determination of optimal sample preparation protocols is often not possible. METHODS: Employing an automated sample preparation quality assessment method recently presented by us we quantified the sample preparation quality obtained using various sample preparation protocols...

RATIONALE: Isoacteoside (ISAT), a phenylethanoid glycoside, acting as the principal bioactive component in traditional Chinese medicines, possesses broad pharmacological effects such as neuroprotective, antihypertensive and hepatoprotective activities. However, its pharmaceutical development has been severely limited due to the poor oral bioavailability. It is essential and significant to investigate related hurdles leading to the poor bioavailability of isoacteoside. METHODS: Whole animal metabolism studies were conducted in rats, followed by metabolic mechanism including gastrointestinal stability, intestinal flora metabolism and intestinal enzyme metabolism employing the powerful ultra-high performance liquid chromatography equipped with quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF-MS)...

RATIONALE: An "Open Access" - like mass spectrometric platform to fully utilize the simplicity of the manual open port sampling interface for rapid characterization of unprocessed samples by liquid introduction atmospheric pressure ionization mass spectrometry has been lacking. The in-house developed integrated software with a simple, small and relatively low-cost mass spectrometry system introduced here fills this void. METHODS: Software was developed to operate the mass spectrometer, to collect and process mass spectrometric data files, to build a database and to classify samples using such a database...

RATIONALE: MALDI-MS has been used for bacterial profiling. A few reports have shown MALDI-MS profiling of cultured cyanobacteria; however, these applications have been limited. In this study, we have investigated whether rapid profiling and differentiation of cyanobacteria including harmful genera Microcystis and Anabaena (Dolichospermum) can be performed by MALDI Biotyper analysis of intact cells. METHODS: Twenty-two cyanobacterial strains including 12 Microcystis, 7 Anabaena, 1 Pseudanabaena, 1 Planktothrix, and 1 Synechocystis, were cultured...

RATIONALE: The goal of this work is the comparison of differences in the lipidomic compositions of human cell lines derived from normal and cancerous breast tissues, and tumor vs. normal tissues obtained after the surgery of breast cancer patients. METHODS: Hydrophilic interaction liquid chromatography - electrospray ionization mass spectrometry (HILIC/ESI-MS) method using the single internal standard approach and response factors is used for the determination of relative abundances of individual lipid species from 5 lipid classes in total lipid extracts of cell lines and tissues...

RATIONALE: Electrospray mass spectrometry methods for the analysis of phosphatidylcholines (PCs) routinely include ammonium acetate or ammonium formate in the mobile phase. In an effort to justify and optimize the use of these additives, we investigated possible functions of ammonium compounds in the ionization of PCs. METHODS: Because PCs contain a quaternary amine, the role of ammonium in neutralizing the negatively charged phosphate group was investigated by using deuterated ammonium acetate, adjusting the pH, varying the organic solvent composition, and by comparing the additives ammonium acetate, ammonium formate and ammonium bicarbonate...

RATIONALE: The ability to recover the isotopic signature of water added to soil samples that have previously been oven dried decreases with the increasing presence of silt and clay. The effects on the isotopic signature of water associated with physicochemical soil properties are not yet fully understood, for either hydration or dehydration of soil samples. METHODS: The soil sample chemistry and the crystallinity of minerals were measured by X-ray fluorescence and X-ray diffraction...

RATIONALE: Steviol glycosides with an ent-kaurene core are being used in the Food Industry as non-caloric sweeteners. These compounds are chemically similar in terms of sugar types and sugar arrangements. In order to assign sugar positions, we describe herein, the dissociation pattern for steviol glycosides under varying collision energies. METHODS: Steviol glycosides (1 mg/mL, 2 μL) were automatically injected into the mass spectrometer by direct infusion using a 100-well tray autosampler...

RATIONALE: Bone lipid compound-specific isotope analysis (CSIA) and bone collagen and apatite stable isotope ratio analysis are important sources of ecological and paleodietary information. Pressurized liquid extraction (PLE) is quicker and utilizes less solvent than traditional methods of lipid extraction such as soxhlet and ultrasonication. This study facilitates dietary analysis by optimizing and testing a standardized methodology for PLE of bone cholesterol. METHODS: Modern and archaeological bone were extracted by PLE using varied temperatures, solvent solutions, and sample weights...

RATIONALE: Ideal biomarkers are present in readily accessible samples including plasma and CSF, and are directly derived from diseased tissue, therefore likely to be of relatively low abundance. Traditional unbiased proteomic approaches for biomarker discovery have struggled to detect low abundance markers due to the high dynamic range of proteins, the predominance of hyper-abundant proteins, and the use of data-dependent acquisition MS. To overcome these limitations and improve biomarker discovery in peripheral fluids, we have developed TMTcalibrator™; a novel MS workflow combining isobarically labelled diseased tissue digests in parallel with an appropriate set of labelled body fluids to increase the chance of identifying low abundance, tissue-derived biomarkers...

RATIONALE: Bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics to identify proteins from a sequence database. De novo sequencing is also available for sequencing peptides with relatively short sequence lengths. We recently showed that paired Lys-C and Lys-N proteases produce peptides of identical mass and similar retention time, but different tandem mass spectra. Such parallel experiments provide complementary information, and allow for up to 100% MS/MS sequence coverage...

RATIONALE: In a bid to develop a mass spectrometer using ac frequency scanning for ion isolation, ion activation, and ion ejection, we have developed scan functions for each process using the inverse Mathieu q scan. METHODS: Ion isolation is accomplished by frequency hopping, that is, by skipping past the ranges of frequencies corresponding to the ions to be isolated during the frequency sweep. Multigenerational collision-induced dissociation is demonstrated by scanning the frequency of excitation from low to high so that multiple generations of product ions can be observed in the product ion mass spectra...

RATIONALE: Many MS2 spectra in bottom-up proteomics experiments remain unassigned. To improve proteome coverage, we applied the half decimal place rule (HDPR) to remove non-peptidic molecules. The HDPR considers the ratio of the digits after the decimal point to the full molecular mass and results in a relatively small permitted mass window for most peptides. METHODS: First, the HDPR mass filter was calculated for the human and other proteomes. Subsequently, the HDPR was applied to three technical replicates of an in-solution tryptic digest of HeLa cells which were analysed by LC-MS using a quadrupole-orbitrap mass spectrometer (Q Exactive)...

RATIONALE: [Cu(P)4 ][BF4 ]-type complexes (P = tertiary phosphine) have shown significant antitumor activity. This biological property appears to be activated via formation of coordinative unsaturated [Cu(P)n ](+) species (n < 4), that may interact with various molecules starting from the solvent(s) in which they are dissolved. Aim of our study was to investigate the interaction of these species with different solvent mixtures. METHODS: The interaction has been investigated in electrospray ionization mass spectrometry, and the interaction products have been characterized by multiple collisional experiments, using an ion trap mass instrument...

RATIONALE: In quantitative analysis of protein biomarkers and therapeutic proteins by liquid chromatography-mass spectrometry (LC-MS), it is a preferred and well-established approach to digest with proteolytic enzymes to produce smaller peptide fragments which are more suitable for LC-MS analysis than the intact protein. In-solution digestion is one widely used method for protein digestion. Proteolytically resistant proteins often require digestion times that extend beyond normal working hours and prohibit same day analysis...

RATIONALE: Mass spectrometry-based protein identification depends mainly on protein extraction and digestion. Although sodium dodecyl sulfate (SDS) can preclude enzymatic digestion and interfere with mass spectrometry analysis, it is still the most widely used surfactant in these steps. To overcome these disadvantages, a SDS-compatible proteomic technique for SDS removal prior to mass-spectrometry-based analyses was developed, namely filter-aided sample preparation (FASP). METHODS: Herein, based on the effectiveness of sodium deoxycholate and detergent removal spin column, we developed a modified FASP (mFASP) method and compared its overall performance, total number of peptides and proteins identified for shotgun proteomic experiments with that of FASP method...